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fSuSiE affected genomic regions

Source: R/AllGenerics.R, R/AllClasses.R
fsusieAffectedRegions.Rd

The sub-intervals of the functional grid where a credible set's band excludes zero (the genomic footprint of each fSuSiE effect), from the upstream fsusieR::affected_reg. Returns a GRanges with the credible-set label, its purity, and the effect direction ("pos"/"neg"; upstream discards it). Requires an UNtrimmed fit; empty otherwise.

Usage

fsusieAffectedRegions(x, ...)

# S4 method for class 'FineMappingResultBase'
fsusieAffectedRegions(x, ...)

Arguments

x

A FineMappingRow or FineMappingResultBase.

...

Ignored.

Value

A GRanges of affected intervals with mcols cs, purity, direction (plus entry identity for the collection).

See also

fsusieCredibleBand

Examples

data(fsusieFineMappingExample)
fsusieAffectedRegions(fsusieFineMappingExample)
#> GRanges object with 4 ranges and 6 metadata columns:
#>       seqnames    ranges strand |          cs    purity   direction
#>          <Rle> <IRanges>  <Rle> | <character> <numeric> <character>
#>   [1]    chr22       1-8      * |    fsusie_1      0.85         pos
#>   [2]    chr22      9-16      * |    fsusie_1      0.85         neg
#>   [3]    chr22       2-8      * |    fsusie_2      0.85         pos
#>   [4]    chr22      9-15      * |    fsusie_2      0.85         neg
#>                  study     context                  trait
#>            <character> <character>            <character>
#>   [1] protocol_example methylation chr22_15528191_15529..
#>   [2] protocol_example methylation chr22_15528191_15529..
#>   [3] protocol_example methylation chr22_15528191_15529..
#>   [4] protocol_example methylation chr22_15528191_15529..
#>   -------
#>   seqinfo: 1 sequence from an unspecified genome; no seqlengths